Execluding some species from training

[m-a-saleh]

Dear developers,

I have a Si slab with varying thickness t_si and whose top and bottom surfaces are passivated by "H" atoms. I need to train an SGP model on AIMD data for it. Training the model on the AIMD data with the two species (H & Si) gives a positive likelihood. However, I think that excluding the "H" atoms from the training will lead to a more accurate trained model as I am interested only in the forces on Si atoms.

To exclude the "H" atoms, I have tried the following, which all resulted in a negative likelihood: -Remove lines starting with "H" from the AIMD.xyz file for all frames -Assign zero forces to "H" atoms in the AIMD.xyz file -Use small cutoffs in cutoff_matrix for "H" (e.g, ctuoff_matrix = [[1.0, 1.0], [1.0, 5.0]])

Any idea on how to exclude those surface "H" atoms?

Thanks